LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -42.647167 0.0000000) to (52.231900 42.647167 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9693600 5.4832072 5.8858683 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -42.647167 0.0000000) to (52.231900 42.647167 8.8288024) create_atoms CPU = 0.003 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9693600 5.4832072 5.8858683 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -42.647167 0.0000000) to (52.231900 42.647167 8.8288024) create_atoms CPU = 0.003 seconds 1690 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 28 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3356 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_304347095149_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.669 | 5.669 | 5.669 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10024.326 0 -10024.326 235675.37 421 0 -14237.153 0 -14237.153 -700.52254 Loop time of 94.6604 on 1 procs for 421 steps with 3356 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10024.3263024314 -14237.1388983023 -14237.1525090288 Force two-norm initial, final = 4035.5370 0.39074980 Force max component initial, final = 358.30695 0.10442597 Final line search alpha, max atom move = 1.0000000 0.10442597 Iterations, force evaluations = 421 756 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 94.027 | 94.027 | 94.027 | 0.0 | 99.33 Neigh | 0.41364 | 0.41364 | 0.41364 | 0.0 | 0.44 Comm | 0.085896 | 0.085896 | 0.085896 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1342 | | | 0.14 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7958.00 ave 7958 max 7958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258496.0 ave 258496 max 258496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258496 Ave neighs/atom = 77.025030 Neighbor list builds = 18 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 421 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.668 | 5.668 | 5.668 Mbytes Step Temp E_pair E_mol TotEng Press Volume 421 0 -14237.153 0 -14237.153 -700.52254 39333.067 433 0 -14240.986 0 -14240.986 3.7979582 39311.278 Loop time of 1.96107 on 1 procs for 12 steps with 3356 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14237.1525090288 -14240.9855955251 -14240.9858398635 Force two-norm initial, final = 523.33277 1.5989566 Force max component initial, final = 383.29629 0.59609921 Final line search alpha, max atom move = 0.00036200357 0.00021579004 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9512 | 1.9512 | 1.9512 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011384 | 0.0011384 | 0.0011384 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008764 | | | 0.45 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7978.00 ave 7978 max 7978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 257942.0 ave 257942 max 257942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257942 Ave neighs/atom = 76.859952 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.804 | 5.804 | 5.804 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14240.986 0 -14240.986 3.7979582 Loop time of 2.53e-06 on 1 procs for 0 steps with 3356 atoms 158.1% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.53e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7909.00 ave 7909 max 7909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258704.0 ave 258704 max 258704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258704 Ave neighs/atom = 77.087008 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 17 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.804 | 5.804 | 5.804 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -14240.986 -14240.986 51.708925 85.192939 8.9237635 3.7979582 3.7979582 -9.271126 24.26583 -3.6008297 2.2659037 12209.768 Loop time of 2.596e-06 on 1 procs for 0 steps with 3356 atoms 308.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.596e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7909.00 ave 7909 max 7909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129352.0 ave 129352 max 129352 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258704.0 ave 258704 max 258704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258704 Ave neighs/atom = 77.087008 Neighbor list builds = 0 Dangerous builds = 0 3356 -14240.9858398635 eV 2.26590371693412 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:37